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revision 1.6, Thu Jun 9 19:06:55 2005 UTC revision 1.12, Tue Sep 13 03:50:59 2005 UTC
# Line 25  Line 25 
25                          the user's access codes must match this value.</Notes>                          the user's access codes must match this value.</Notes>
26                                          <DataGen>RandParam('low','medium','high')</DataGen>                                          <DataGen>RandParam('low','medium','high')</DataGen>
27                  </Field>                  </Field>
28                    <Field name="complete" type="boolean">
29                        <Notes>TRUE if the genome is complete, else FALSE</Notes>
30                    </Field>
31                                  <Field name="taxonomy" type="text">                                  <Field name="taxonomy" type="text">
32                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements                                          <Notes>The taxonomy string contains the full taxonomy of the organism, while individual elements
33                                          separated by semi-colons (and optional white space), starting with the domain and ending with                                          separated by semi-colons (and optional white space), starting with the domain and ending with
# Line 98  Line 101 
101                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>                                          <DataGen>RandChars("ACGT", IntGen(100,400))</DataGen>
102                                  </Field>                                  </Field>
103                  <Field name="quality-vector" type="text">                  <Field name="quality-vector" type="text">
104                                          <Notes>String describing the quality data for each . Individual values will                      <Notes>String describing the quality data for each base pair. Individual values will
105                                          be separated by periods. The value represents negative exponent of the probability                                          be separated by periods. The value represents negative exponent of the probability
106                                          of error. Thus, for example, a quality of 30 indicates the probability of error is                                          of error. Thus, for example, a quality of 30 indicates the probability of error is
107                                          10^-30. A higher quality number a better chance of a correct match. It is possible                                          10^-30. A higher quality number a better chance of a correct match. It is possible
108                                          that the quality data is known for a sequence. If that is the case, the quality                      that the quality data is not known for a sequence. If that is the case, the quality
109                                          vector will contain the [b]unknown[/b].</Notes>                                          vector will contain the [b]unknown[/b].</Notes>
110                                          <DataGen>unknown</DataGen>                                          <DataGen>unknown</DataGen>
111                                  </Field>                                  </Field>
# Line 119  Line 122 
122                                          <DataGen>RandParam('peg','rna')</DataGen>                                          <DataGen>RandParam('peg','rna')</DataGen>
123                                  </Field>                                  </Field>
124                  <Field name="alias" type="name-string" relation="FeatureAlias">                  <Field name="alias" type="name-string" relation="FeatureAlias">
125                                          <Notes>Alternative name for this feature. feature can have many aliases.</Notes>                      <Notes>Alternative name for this feature. A feature can have many aliases.</Notes>
126                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>                                          <DataGen testCount="3">StringGen('Pgi|99999', 'Puni|XXXXXX', 'PAAAAAA999')</DataGen>
127                                  </Field>                                  </Field>
128                  <Field name="translation" type="text" relation="FeatureTranslation">                  <Field name="translation" type="text" relation="FeatureTranslation">
129                                          <Notes>[i](optional)[/i] A of this feature's residues into character codes, formed by concatenating                      <Notes>[i](optional)[/i] A translation of this feature's residues into character
130                          the pieces of the feature together.</Notes>                      codes, formed by concatenating the pieces of the feature together. For a
131                        protein encoding group, this is the protein characters. For other types
132                        it is the DNA characters.</Notes>
133                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
134                                  </Field>                                  </Field>
135                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">                  <Field name="upstream-sequence" type="text" relation="FeatureUpstream">
# Line 133  Line 138 
138                                          <DataGen testCount="0"></DataGen>                                          <DataGen testCount="0"></DataGen>
139                                  </Field>                                  </Field>
140                  <Field name="active" type="boolean">                  <Field name="active" type="boolean">
141                                          <Notes>TRUE if this feature is still considered valid, if it has been logically deleted.</Notes>                      <Notes>TRUE if this feature is still considered valid, FALSE if it has been logically deleted.</Notes>
142                                          <DataGen>1</DataGen>                                          <DataGen>1</DataGen>
143                                  </Field>                                  </Field>
144                                  <Field name="link" type="text" relation="FeatureLink">                                  <Field name="link" type="text" relation="FeatureLink">
# Line 144  Line 149 
149                                          "&amp;Number=" . IntGen(1,99)</DataGen>                                          "&amp;Number=" . IntGen(1,99)</DataGen>
150                                  </Field>                                  </Field>
151              </Fields>              </Fields>
152                <Indexes>
153                    <Index>
154                        <Notes>This index allows the user to find the feature corresponding to
155                        the specified alias name.</Notes>
156                        <IndexFields>
157                            <IndexField name="alias" order="ascending" />
158                        </IndexFields>
159                    </Index>
160                </Indexes>
161          </Entity>          </Entity>
162          <Entity name="Role" keyType="string">          <Entity name="Role" keyType="string">
163              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.              <Notes>A [i]role[/i] describes a biological function that may be fulfilled by a feature.
# Line 334  Line 348 
348                      to decode that relationship. Currently, this field is either "1" or                      to decode that relationship. Currently, this field is either "1" or
349                      "2".</Notes>                      "2".</Notes>
350                  </Field>                  </Field>
                 <Field name="percentMatch" type="float">  
                     <Notes>Percent similarity between our target feature and the  
                     corresponding feature of the coupling.</Notes>  
                 </Field>  
                 <Field name="paralogs" type="int">  
                     <Notes>Number of features on the same genome that are analogous  
                     to our target feature. A higher paralog count indicates less  
                     valuable evidence.</Notes>  
                 </Field>  
351              </Fields>              </Fields>
352              <FromIndex>              <FromIndex>
353                  <Notes>This index enables the application to view the features of                  <Notes>This index enables the application to view the features of

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